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Literature summary for 1.5.99.15 extracted from
- Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer (2014), J. Biol. Chem., 289, 8852-8864 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| expressed in Escherichia coli BL21 (DE3)-RIL cells | Paraburkholderia xenovorans |
| gene dmrB, recombinant expression of N-terminally His6 -tagged enzyme in Escherichia coli strain BL21DE3 RIL | Paraburkholderia xenovorans |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| hanging drop vapor diffusion method, using 0.8-1.2 M ammonium sulfate as precipitant | Paraburkholderia xenovorans |
| purified recombinant N-terminally His6 -tagged enzyme by hanging drop vapor diffusion method, mixing of 0.003 ml of 13 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 100 mM NaCl, 5% glycerol, and 4 mM DTT, with reservori solution containing FMN, method optimization, 7-14 days at room temperature, X-ray diffraction structure determination and analysis at 1.9 A resolution | Paraburkholderia xenovorans |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 5,6,7,8-tetrahydromethanopterin + oxidized acceptor | Paraburkholderia xenovorans | - |
7,8-dihydromethanopterin + reduced acceptor | - |
? |  |
| 7,8-dihydromethanopterin + FMNH2 | Paraburkholderia xenovorans | - |
5,6,7,8-tetrahydromethanopterin + FMN | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Paraburkholderia xenovorans | Q13QT8 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| HisTrap column chromatography and S200 gel filtration | Paraburkholderia xenovorans |
| recombinant N-terminally His6 -tagged enzyme from Escherichia coli strain BL21DE3 RIL cell-free extract by nickel affinity chromatography and gel filtration | Paraburkholderia xenovorans |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| 5,6,7,8-tetrahydromethanopterin + oxidized acceptor = 7,8-dihydromethanopterin + reduced acceptor | DmrB uses a ping-pong mechanism to transfer reducing equivalents from FMN to the pterin substrate, modeling, overview | Paraburkholderia xenovorans |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 5,6,7,8-tetrahydromethanopterin + oxidized acceptor | - |
Paraburkholderia xenovorans | 7,8-dihydromethanopterin + reduced acceptor | - |
? | |
| 7,8-dihydromethanopterin + FMNH2 | - |
Paraburkholderia xenovorans | 5,6,7,8-tetrahydromethanopterin + FMN | - |
? | |
| 7,8-dihydromethanopterin + FMNH2 | DmrB uses a ping-pong mechanism to transfer reducing equivalents from FMN to the pterin substrate, identification of the 7,8-dihydromethanopterin binding site by computational docking | Paraburkholderia xenovorans | 5,6,7,8-tetrahydromethanopterin + FMN | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| homotetraicosamer | 24 * 22100, His6-tagged enzyme, SDS-PAGE | Paraburkholderia xenovorans |
| homotrimer | enzyme crystal structure analysis | Paraburkholderia xenovorans |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| dihydromethanopterin reductase | - |
Paraburkholderia xenovorans |
| Dmr | - |
Paraburkholderia xenovorans |
| DmrB | - |
Paraburkholderia xenovorans |
| H2MPT reductase | - |
Paraburkholderia xenovorans |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| FMN | - |
Paraburkholderia xenovorans | |
| FMN | within a homotrimer, each monomer-monomer interface exhibits an active site with two adjacently bound flavin mononucleotide (FMN) ligands, one deeply buried and tightly bound and one more peripheral. Computational docking suggests that the peripheral site binds either the observed FMN (the electron donor for the overall reaction) or the pterin, H2MPT (the electron acceptor for the overall reaction), in configurations ideal for electron transfer to and from the tightly bound FMN. Analysis of the FMN binding structure in the active site, and kinetics, overview | Paraburkholderia xenovorans | |
| additional information | determination of FMN is the cofactor of DmrB, overview | Paraburkholderia xenovorans |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | sequence comparisons suggested that the catalytic mechanism is conserved among the bacterial homologues of DmrB and partially conserved in archaeal homologues, where an alternate electron donor is likely used | Paraburkholderia xenovorans |
| metabolism | the enzyme catalyzes the final step of methanopterin biosynthesis | Paraburkholderia xenovorans |
| physiological function | dihydromethanopterin reductase (Dmr) is a redox enzyme that plays a key role in generating tetrahydromethanopterin (H4MPT) for use in one-carbon metabolism. DmrB is a bacterial enzyme that reduces dihydromethanopterin (H2MPT) to H4MPT using flavins as the source of reducing equivalents | Paraburkholderia xenovorans |
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